The Atlantis Variation
by SomewhereBeyondReality
Summary: What happened to the other John in the Deadlaus variation? What happened to his Atlantis?


_**The Atlantis Variation**_

"...you're obviously a man of great integrity, and a dedicated commander and a very skilled pilot." The voice over the radio came.

"Well that's funny, I was going top say the same to you," replied Lieutenant Colonel John Sheppard as he guided his F-302 fighter jet back away from the battered ship.

Throwing a casual wave at the vanishing Deadalus, John flew down towards Atlantis. The Jumper Bay doors folded open in their usual graceful motion and he shot into the high vaulted room and skidded to a halt just before he hit the ground. Not before he'd slid under the shelf of Jumper Three and parked the F-302 did John finally allow himself to rip off the goggles. Letting out a deep breath the radio activated, "Atlantis, this is Sheppard. We have successfully disabled the alien ship."

"Good to hear that John." The commander said, their voice clipped with stress.

"Getting worried huh?" He guessed, recognising the tone.

"Just glad you're home safe." Elizabeth answered quietly into her radio, moving away from Chuck and the other technicians. "Now get down here."

Elizabeth demanded a debriefing the moment they all touched the ground. It was short, because to be honest there wasn't much to tell. She knew that a couple of hours earlier the Deadalus (which was meant to be shot to pieces by the Replicators) had appeared out of nowhere and fired at the unidentified alien ship in orbit which was about to blast them into little pieces of debris floating on the rippling water. It had vanished before they could contact it and appeared again not long later in bad condition. She'd authorised him to go take the fleet of F-302's to defend it. The grateful crew had said thanks, bye and vanished again. End of story. Even she couldn't suck much life out of that one.

The only thing that was remotely interesting, John mused thoughtfully, as another officer began to speak, (apart from the obvious adrenaline rush of whirling around in a jet, shooting stuff) was the person on board of the resurrected Deadalus. They hadn't been able to talk long and the connection hadn't been great but even he could recognise his own voice. For a minute he'd wondered if he had taken a hard hit without noticing but just gave in. This was Pegasus. Besides, no one else would bother to compliment him that much.

"Alright thank you," Elizabeth nodded to the rest of the pilots and they filed out of the conference room. John stayed where he was, propping his feet up on the table.

"So, what theory had Rodney got this time?" He asked, as Elizabeth slipped into the chair beside him and started arranging the papers into perfect rectangles.

She flashed him a small smile, "he was tossing up between a visit from the past or alternate universe, and I think he decided they were from another universe." She leaned back, rubbing her forehead; "but I guess we'll never know."

"Well, I'm willing to go with Rodney on this one," John said, "seems cooler and I've had enough of travelling in time." He cringed as he remembered stepping through the gate to an empty, abandoned Atlantis, thousands of years into the future. It would take a long time to get that vision out of his head.

Elizabeth glanced at him, her eyes soft and understanding; she knew him too well. He looked back at her, suddenly overcome with an unexpected wave of emotion. It had been just over a year ago when she'd been lying in that hospital bed and he'd been gazing at her through a plastic sheet, certain she would bound for death, or a life where she was only a shell of the person she once was.

John had had to face the reality of a life without her.

And he couldn't take it. He didn't want to survive in Atlantis if she wasn't there. In fact, he wasn't sure he wanted Atlantis to survive if she wasn't there.

Then Rodney and Jennifer had reactivated her nanites cells. He'd been trapped between wanting to kill them for defying his orders – the orders he knew Elizabeth would have given – and promoting both of them for bringing her back. Not that he'd shown that.

It turned out to be the best thing they could have done. With Elizabeth able to connect to replicators, they'd been able to retrieve a ZPM from the replicators and save the city. Straight in, straight out.

There'd been problems afterwards obviously. Entanglements with red tape and the possibility of losing Elizabeth through rules and regulations instead of death. But with time and the guarantee that her nanites cells were completely under control; life had returned to normal.

It still shocked him sometimes. Shocked him at how lucky he was that they were all still around; safe in Atlantis.

John shook himself and focused back into life. "Do you want to come up to the Mess and grab something to eat?" He asked, yawning as he stood up.

"Sure," Elizabeth replied, quickly getting to her feet.

She followed him out and made her way through the control room, not noticing that their paces, over time had become perfectly matched, so the two of them walked in perfect rhythm, her legs stretching and his longer strides shortening so they walked as one. The passages were quiet; no doubt the crowing pilots were quickly spreading the news around that they'd just saved Atlantis from certain doom. It was reaching twilight and the built-in lights (whose bulbs mysteriously never needed to be changed) had lit up. Studded along the carved bronze walls, this section coloured in alternating gentle blues and yellows they gave the empty corridor a curiously cosy feel.

John's hand brushed lightly against hers making her give an inward start as if a spark of electricity had leapt between them in that brief moment of connection. Stealing a glance at him Elizabeth caught him staring back. She raised one eyebrow and let out a silent laugh; he grinned sheepishly back and gave a slight grimace before turning away to as if the floor had suddenly become a subject of great fascination.

More and more these days Elizabeth seemed to find herself looking at him like that, and she knew she wasn't the only one. She couldn't count the number of times she'd caught John's gaze fixed on her, tender and passionate all at once. Whenever she did her stomach would writher uncontrollably and she'd find herself sucked into a whirlwind of emotions.

Fear. Caution. Frustration. And an unidentifiable feeling; stronger than all the rest put together.

No matter how deep she tried to push it; it kept springing back up until she didn't have the strength to bury it anymore – only conceal. Elizabeth knew that it was dangerous; even stupid, idiotic, to let this continue, but didn't she deserve to let herself go for once? Allow herself some sort of life? The two of them had both been through so much; putting Atlantis first and foremost, time and time again. Sacrificing one another for the "greater good." For now, Elizabeth was going to step forward and Doctor Weir would take the backseat.

And they'd both watch and see what happened.

"Do you really think they were from an alternate reality?" She asked she waved her hand in front of a transporter sensor.

John shrugged, "no idea, wouldn't be the first time; but it was definitely me on the other end. Didn't have time to ask questions."

A hard, cold knot of worry formed in her stomach, "we did do the right thing though," she said trying to sound confident, "to help them"

John rolled his eyes, as they stepped inside and he pressed the location they wanted to go, the doors slide smoothly shut and he turned to her. "They saved our asses back there, as far as I'm concerned that's good enough for me and the least we could do is return the favour."

She nodded, as they got out and headed into the mess, "yes, of course, I just meant..."

"Elizabeth," John groaned, grabbing a tray, "for once in your life quit worrying! Yes it could turn out to be my evil twin and trust me that would be ugly. Yes, the Wraith could come banging on our doorstep any day now. Yes more of those alien ships could turn up. Yes, you could fall off the pier and drown tomorrow! You can't do anything about it so," he handed her a tub of jello, "eat, drink and be merry." Now he showed off that famous, cocky flyboy grin.

She gave him one of her looks and it wilted. "Shakespeare?"

"No idea, good quote though." He said, dragging a chair over to a small table by the window and plonking himself down.

"Ok, ok." Elizabeth sighed, "But I was just thinking –"

"Don't" John said through a mouthful of roll, "very dangerous thing to do."

"Not that you would know that," She retorted sitting down opposite him.

John shot her a wounded look, "I have my moments."

"Just very few and far between." She said, spearing a piece of pasta on the fork and popping it in her mouth.

"You're getting more like Rodney everyday, you know that?" he said, "Alright, I give up, too tired." He took a sip of juice before spluttering, "and don't give me that look!" He snapped.

Elizabeth smiled sweetly, "I didn't say a thing." He just grunted.

They ate in silence for a couple of minutes, watching the waves break through the wide, floor to ceiling window by their table. A covered walkway scattered with plants and potted trees ran along the side of the mess.

"So," John said, breaking the silence, "_do_ you think they were from an alternate reality?"

"I wouldn't be surprised," Elizabeth said, sipping her drink and looking at him over her glass, her eyes piercing. John felt him stomach roll, not in a bad way, just the sort of I've-just-ridden-something-that-goes-faster-that-200-miles-an-hour way; only slightly rougher.

"So," She continued, smiling slightly. "Alternate universe, what would you want to change?"

John sighed and raised his eyes heavenward, "Elizabeth, you know how great I am with these theoretical questions."

"Yes, I know you struggle to relate to anything that isn't solid and needs shooting," she teased, "but seriously, what would you want to be different?"

John was about to come up with a witty retort when he stopped. What would he change?

His father's death? That hadn't been great, but he'd lived a long life. Maybe he wished that they'd been closer, forgiven each other sooner, but he was seeing Dave again, that was good.

Ford leaving? Yeah he'd always regret that but they had Ronon now and there was always a chance...

Carson dying? Except he hadn't, not really.

His marriage to Nancy? That hadn't turned out so well but in a way John had accepted it; you moved on, he wasn't sure he wanted to just erase all those times.

To his surprise the most unexpected answer came out. "Well, right now, I don't think I'd change anything" He said.

Elizabeth put down her spoon; her eyes now alight with interest and curiosity. "Really? You wouldn't change a thing?"

John shook his head, "nope, at this moment I think life is just fine the way it is."

"You wouldn't even want the Wraith to be gone?"

"Alright, I'll give you that," he admitted, "alternate universe just like this but with no Wraith. Sounds good to me, although," he frowned, "a little boring."

Elizabeth laughed and John turned once more to look out of the window. Dark clouds had begun to gather in the grey sky and heavy raindrops fell on the tiles outside. Despite this narrow rays of sunlight had managed to fight their way through and shone down on Atlantis; faint, but warm.

"I wonder what their universe was like though." Elizabeth wondered aloud.

"Yeah," John echoed, "I wonder what it was like."

A whole world away, Lieutenant Colonel John Sheppard stood alone on a lonely balcony watching wild storm clouds fill the sky without the faintest sun beam to light his day. "I wonder," He murmured, as ice cold droplets started to splatter him, soaking him to the skin. "I wonder what his universe was like?" Turning away from the view he vanished inside, leaving an empty space behind him, as if he had never been there.

One thing he knew with certainty; the other's world had to be better than this one.


End file.
